I did a direct comparison last summer, although it wasn't precisely in my system. It was at my dealer, who used a similar system. He had two Classe CAM-200s instead of my single CA-200, a Classe CP65 preamp instead of my SSP-75 prepro, my actual turntable - I bought it then - and Cardas Golden Reference instead of Neutral Reference cables. His listening room is definitely set up a mile better than my temporary quarters.
I basically could not tell the difference in the panels. I think the Prodigy might have been ever so slightly better in the highest end, but the difference was small enough that I at least could not be sure that it was there, let alone significant. I would call the Odyssey at least 99% of the Prodigy in this area.
There is definitely difference in the cones. The Prodigy moves more air and goes lower, precisely as you'd expect from its bigger drivers. However, the Odyssey is no slouch and it is distinctly FASTER and a little tighter. I think the Odyssey integrates better because its cones are faster, although I think it's better because of the speed rather than the integration.
I was in a quandry until the next time I came around, when the Descent subwoofer was hooked up for the previous listener (who was listening to a different speaker). The Descent uses the same smaller, faster drivers as the Odyssey, but REALLY puts out the bass. So we changed plans and compared the Odyssey + Descent to the Prodigy, and the answer was crystal clear. The sub setup had all of the speed of the smaller drivers, and significantly better overall bass. Since the Odyssey + Descent combination costs around the same as the Prodigy by itself, this was a nobrainer in the end.